During the past two decades, chemically modified oligodeoxynucleotides (ODNs) have received much attention in search for potential therapeutic and diagnostic agents and in the study of numerous biochemical and biological processes. The use of modified ODNs as specific targeting of gene expression has become an indispensable tool in antisense research. There has been a revival of interest in gene silencing since the discovery that short interfering RNA (siRNA) molecules can affect RNA interference in mammalian cells.
ODNs have been extensively modified in order to enhance their stability to nuclease, cell penetration ability, selectivity, binding affinity toward complementary nucleic acids, and the melting temperature (Tm) of formed duplex. To a great extent, these modifications have focused on replacing the phosphodiester group or the whole deoxysugar-phosphodiester backbone with alternative anionic, cationic, and neutral structures. Some examples include using peptide nucleic acid (PNA), bicyclic oligonucleotides as locked nucleic acids (LNA), modified sugars such as hexitol nucleic acid (HNA), and phosphodiester mimics.
A number of phosphodiester mimics have been synthesized by replacing the phosphate group. These phosphodiester mimics include phosphorothioate, methylphosphate, phosphoramidates, boranophosphate, alkylphosphotriesters, phosphorodithioate, phosphonomethyl, propynes, diene, phosphonoformate, and other groups. The phosphate-modified DNA oligomers have been extensively used in biological research as inhibitors of gene expression, viral enzymes such as HIV reverse transcriptase, in vitro mRNA translation, and sequence-specific DNA binding proteins when present in duplex form.
Nucleosides are intracellularly converted to nucleoside monophosphates, diphosphates, and triphosphates, respectively, in the presence of kinases. Diphosphorylation and triphosphorylation are required for the synthesis of nucleotides and nucleic acids thus producing biological activity of all nucleosides, as shown in several antiviral and anticancer drugs.